Strain identifier

BacDive ID: 297

Type strain: Yes

Species: Achromobacter xylosoxidans

Strain Designation: KM543

Strain history: CIP <- 1971, E. Yabuuchi, Osaka, Japan: strain KM 543, Achromobacter xylosoxidans

NCBI tax ID(s): 85698 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 1075

BacDive-ID: 297

DSM-Number: 2402

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Achromobacter xylosoxidans KM543 is an aerobe, mesophilic, motile bacterium that was isolated from ear discharge.

NCBI tax id

  • NCBI tax id: 85698
  • Matching level: species

strain history

@refhistory
364891971, E. Yabuuchi, Osaka, Japan: strain KM 543, Achromobacter xylosoxidans
1075<- ATCC <- Eiko Yabuuchi, KM543 (Achromobacter xylosoxidans)
67770R. Hugh 2838.
124002CIP <- 1971, E. Yabuuchi, Osaka, Japan: strain KM 543, Achromobacter xylosoxidans

doi: 10.13145/bacdive297.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Achromobacter
  • species: Achromobacter xylosoxidans
  • full scientific name: Achromobacter xylosoxidans (ex Yabuuchi and Ohyama 1971) Yabuuchi and Yano 1981
  • synonyms

    @refsynonym
    20215Achromobacter xylosoxidans
    20215Alcaligenes xylosoxidans
    20215Alcaligenes xylosoxydans
    20215Alcaligenes denitrificans subsp. xylosoxydans

@ref: 1075

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Achromobacter

species: Achromobacter xylosoxidans subsp. xylosoxidans

full scientific name: Achromobacter xylosoxidans subsp. xylosoxidans (ex Yabuuchi and Ohyama 1971) Yabuuchi et al. 1998

strain designation: KM543

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.462
6948099.998negative
124002yesnegativerod-shaped

colony morphology

@refincubation period
10751-2 days
124002

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36489MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
1075NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
124002CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
36489positivegrowth30mesophilic
1075positivegrowth30mesophilic
60956positivegrowth37mesophilic
67770positivegrowth30mesophilic
124002positivegrowth15-41
124002nogrowth5psychrophilic
124002nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60956aerobe
124002obligate aerobe

spore formation

@refspore formationconfidence
69481no96
69480no99.859

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
6836817632nitrate+reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12400216947citrate+carbon source
1240024853esculin-hydrolysis
124002606565hippurate+hydrolysis
12400217632nitrate+builds gas from
12400217632nitrate+reduction
12400216301nitrite+builds gas from
12400216301nitrite+reduction
12400235020tributyrin-hydrolysis
12400215792malonate-assimilation
12400217632nitrate+respiration

antibiotic resistance

  • @ref: 124002
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836816301nitriteyes
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12400235581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
6836815688acetoin+
6836835581indole-
12400215688acetoin-
12400217234glucose-

enzymes

@refvalueactivityec
1075catalase+1.11.1.6
1075cytochrome-c oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
124002oxidase+
124002beta-galactosidase-3.2.1.23
124002alcohol dehydrogenase-1.1.1.1
124002gelatinase-
124002amylase-
124002DNase-
124002caseinase-3.4.21.50
124002catalase+1.11.1.6
124002tween esterase-
124002gamma-glutamyltransferase-2.3.2.2
124002lecithinase-
124002lipase-
124002lysine decarboxylase-4.1.1.18
124002ornithine decarboxylase-4.1.1.17
124002phenylalanine ammonia-lyase-4.3.1.24
124002tryptophan deaminase-
124002urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
124002--++-+---++---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2
1075----+----+-----------+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
1075+-------+-+/----+++++++
1075+-------+-----++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
124002+--------------------+---------------------++-++++++++------++---+-------+-++--++++----++++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentisolation date
1075ear discharge
60956Human ear1969OsakaJapanJPNAsia
67770Ear discharge
124002Ear dischargeOsakaJapanJPNAsia1969

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Organ#Ear
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_710.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_9;97_9;98_570;99_710&stattab=map
  • Last taxonomy: Achromobacter
  • 16S sequence: Y14908
  • Sequence Identity:
  • Total samples: 1520
  • soil counts: 273
  • aquatic counts: 362
  • animal counts: 742
  • plant counts: 143

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
10752Risk group (German classification)
1240021Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
1075Achromobacter xylosoxidans 16S rRNA gene, type strain DSM 10346Y149081495ena85698
67770Achromobacter xylosoxidans gene for 16S ribosomal RNAD880051462ena85698

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Achromobacter xylosoxidans NCTC10807GCA_001457475completencbi85698
66792Achromobacter xylosoxidans NBRC 15126 = ATCC 27061GCA_000508285completencbi1216976
66792Achromobacter xylosoxidans NBRC 15126 = ATCC 270611216976.8wgspatric1216976
66792Achromobacter xylosoxidans NBRC 15126 = ATCC 270611216976.3completepatric1216976
66792Achromobacter xylosoxidans strain FDAARGOS_78985698.244completepatric85698
66792Achromobacter xylosoxidans strain NCTC1080785698.28completepatric85698
66792Achromobacter xylosoxidans NCTC108072667527485completeimg85698
66792Achromobacter xylosoxidans NBRC 15126, ATCC 270612558309085completeimg1216976
66792Achromobacter xylosoxidans NBRC 15126, ATCC 270612731957707draftimg1216976
67770Achromobacter xylosoxidans NBRC 15126 = ATCC 27061GCA_001598595contigncbi1216976
67770Achromobacter xylosoxidans genome assembly NCTC10807, chromosome : 1LN831029ncbi85698

GC content

@refGC-contentmethod
107569.2
6777057.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
flagellatedno65.377no
gram-positiveno98.25no
anaerobicno98.726yes
aerobicyes88.836no
halophileno90.813no
spore-formingno93.149no
glucose-utilyes56.314yes
motileyes84.702no
thermophileno99.676yes
glucose-fermentno91.957yes

External links

@ref: 1075

culture collection no.: DSM 2402, ATCC 27061, DSM 10346, NRRL 84082, CCUG 56438, CIP 71.32, NCTC 10807, LMG 1863, CCM 2741, IFO 15126, NCIMB 12033, JCM 9659, CCUG 12689, CECT 467, CECT 927, IAM 12684, NBRC 15126, NRRL B-4082, NCIB 12033

straininfo link

  • @ref: 69979
  • straininfo: 389299

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity6699141Nosocomial colonization and infection by Achromobacter xylosoxidans.Reverdy ME, Freney J, Fleurette J, Coulet M, Surgot M, Marmet D, Ploton CJ Clin Microbiol10.1128/jcm.19.2.140-143.19841984Alcaligenes/*classification/drug effects/metabolism, Anti-Bacterial Agents/pharmacology, Bacterial Infections/*microbiology, Cross Infection/*microbiology, Humans, Male, Microbial Sensitivity Tests, Middle AgedPhylogeny
Phylogeny9688077Emendation of genus Achromobacter and Achromobacter xylosoxidans (Yabuuchi and Yano) and proposal of Achromobacter ruhlandii (Packer and Vishniac) comb. nov., Achromobacter piechaudii (Kiredjian et al.) comb. nov., and Achromobacter xylosoxidans subsp. denitrificans (Ruger and Tan) comb. nov.Yabuuchi E, Kawamura Y, Kosako Y, Ezaki TMicrobiol Immunol10.1111/j.1348-0421.1998.tb02306.x1998Alcaligenes/*classification/genetics, Bacterial Typing Techniques, Bordetella/classification, DNA, Bacterial/analysis/chemistry, Humans, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicPathogenicity
Enzymology14965775Cytoplasmic expression of the Achromobacter xylosoxidans blue copper nitrite reductase in Escherichia coli and characterisation of the recombinant protein.Ho WH, Ooi BL, Jorgensen AM, Borg L, Jespersen LL, Christensen HEProtein Expr Purif10.1016/j.pep.2003.08.0102003Achromobacter denitrificans/*enzymology/genetics, Cytoplasm/enzymology, Electron Spin Resonance Spectroscopy, Escherichia coli/*enzymology/genetics, Nitrite Reductases/*biosynthesis/*chemistry/genetics/isolation & purification, Recombinant Proteins/biosynthesis/genetics/isolation & purification, Spectrometry, Mass, Electrospray Ionization/methods, Spectrophotometry, UltravioletPhylogeny
Phylogeny19671719Parapusillimonas granuli gen. nov., sp. nov., isolated from granules from a wastewater-treatment bioreactor.Kim YJ, Kim MK, Im WT, Srinivasan S, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.009720-02009Alcaligenaceae/classification/*genetics/isolation & purification, Base Sequence, Carboxylic Acids/metabolism, Cell Size, DNA, Bacterial/genetics, Enzymes/metabolism, Glucose/metabolism, Molecular Sequence Data, Phylogeny, Quinones/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsMetabolism
Pathogenicity25487802Genomic insights into intrinsic and acquired drug resistance mechanisms in Achromobacter xylosoxidans.Hu Y, Zhu Y, Ma Y, Liu F, Lu N, Yang X, Luan C, Yi Y, Zhu BAntimicrob Agents Chemother10.1128/AAC.04260-142014Achromobacter denitrificans/*drug effects/*genetics, Anti-Bacterial Agents/*pharmacology, Drug Resistance, Multiple, Bacterial/*genetics, Genome, BacterialGenetics
Phylogeny27902206Achromobacter aloeverae sp. nov., isolated from the root of Aloe vera (L.) Burm.f.Kuncharoen N, Muramatsu Y, Shibata C, Kamakura Y, Nakagawa Y, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0015662017Achromobacter/*classification/genetics/isolation & purification, Aloe/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Ubiquinone/chemistryTranscriptome
Phylogeny28975472Sulfur oxidation by Achromobacter xylosoxidans strain wsp05 reveals ecological widening over which thiotrophs are distributed.Jadhav K, Jadhav IWorld J Microbiol Biotechnol10.1007/s11274-017-2359-62017Achromobacter denitrificans/*classification/genetics/isolation & purification, Environmental Microbiology, Genes, rRNA, Hydrogen-Ion Concentration, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sulfites/chemistry, Sulfur/*chemistry, Temperature, Thiosulfates/chemistryEnzymology
Phylogeny33033853Achromobacter aestuarii sp. nov., Isolated from an Estuary.Kim SC, Chung SO, Lee HJCurr Microbiol10.1007/s00284-020-02231-92020*Achromobacter, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Estuaries, Fatty Acids/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitle
1075Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2402)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2402
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
36489Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10603
60956Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56438)https://www.ccug.se/strain?id=56438
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
69979Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389299.1StrainInfo: A central database for resolving microbial strain identifiers
124002Curators of the CIPCollection of Institut Pasteur (CIP 71.32)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2071.32